Now we have containers, there is a lot of data on the external storage.
For now I use “scp” to backup that storage but it takes long and is always a complete backup.
Any idea for a good practice how to backup the external storage?
Hi!!!
You could consider using a more efficient backup method, such as rsync, which only transfers the differences between the source and destination instead of the entire file. Additionally, you can schedule regular incremental backups using cron jobs to save time and resources. Another option is to use a cloud-based backup solution, such as AWS S3 or Google Cloud Storage, to store your backups securely in the cloud. Finally, it’s important to also keep multiple backups stored in different locations for disaster recovery purposes. 
Mine (not so practical) solution is physically connecting storage on to backup computer and creating backup image of entire file system mounted on ROS each time I change something for containers setup persistence (on mounted directories) or when upgrading container image. It is not too often for my containers so this approach doesn’t bother me and it is much faster than network sync.
Your options improve in 7.7beta3+, Mikrotik support RAID modes and rsync with the new “rose” extra-package:
http://forum.mikrotik.com/t/7-8beta2-adds-new-package-rose-storage/163810/1